Version 1.0.0

First IHEC release

• Whole pipeline refactoring - #51
• Fix wrong merging information - #55
• Add ability to use regex for reference prefix in bigwig step - #17

Additional improvements and fixes:

• Use 2/3 of the process memory in mapping
• Increase quantification memory in IHEC resources config file
• Update sambamba version to 0.7.1
• Update bamstats version to 0.3.4
• Enable autoMounts for Singularity by default
• Add script to prepare input FASTQ files from BAM files
• Fix issue in field order when reading input BAMs
• Add gtf and gff to supported file types in CI script
• Sort transcriptome BAMs before merge
• Remove test.sh, update CI tests and TravisCI configuration file
• Fix workflow for input BAMs and add test profile
• Add threshold option to infer experiment script and add corresponding pipeline parameter
• Fix read group attributes in mapping

IHEC specific changes:

• Move all IHEC documentation to ihec-setup.md, update and clean up
• Clean up pipeline config and use single IHEC image for the IHEC profile
• Add script to pre-fetch the IHEC Singularity image
• Add the IHEC profile to TravisCI config
• Update test data and checksum, add checksums for the IHEC profile

Full Changelog: v0.4.1...v1.0.0

Version 0.4.1

• Fix wrong comment in config file breaking pipeline execution
• Update minimum Nextflow version badge in readme to 0.30.2

Full Changelog: v0.4.0...v0.4.1

Version 0.4.0

• Add mark-duplicates step - #40.
• Convert existing samtools commands in templates to corresponding available sambamba one - #41.
• Add bamStats process - #42
• Add process and logic to download input files - #43
• Support compressed reference files - #44
• Replace groupBy related logic in pipeline script - #46

Additional fixes and improvements

• Add memory limit to sambamba sort command in RSEM quantification step
• Add sort buffer size option in sambamba markdup
• Update container for fetch process
• Update IHEC profile BAM sorting tool
• Update Nextflow and TravisCI config files
• Update gem mapping templates for new version of samtools
• Add nextflow config profiles for IHEC and update TravisCI configuration
• Clean-up into calls using closure syntax
• Set halfCpus as integer and fix it when task.cpus is 1
• Add Dockerfiles
• Update readme and add description of pipeline parameters
• Add Singularity section to readme with tips and troubleshoot
• Update tool versions in readme
• Bump sambamba version to 0.7.0
• Bump tool versions for bamstats, samtools and RSeQC

Full Changelog: v0.3.0...v0.4.0

Version 0.3.0

• Fix #21 - sort index file lines when grouping paired FASTQ files
• Disable Docker by default and update test script - resolve #22
• Update test profiles and main config - address #25
• Move process resource to external config file - #24
• Modified quantification step by removing the temporary sorted bam file. By doing this we can pipe an uncompressed sam file directly to rsem - #26 thanks @karl616
• Fix issue with modified quantification templates - introduced by #26
• Use withName process selector in configuration files - close #39
• Update test script, configuration profiles and checksums - #30
• Add option to enforce strandness - first implementation of #11
• Fix bedgraph filename error in contig template - close #27
• Add tool versions to readme - close #18

Additional fixes and imporvements:

• Change README markup to Markdown
• Update CI configuration
• Improve RGCRG bigwig templates by removing temporary bam files
• Fix missing NH:1 filter in contigs antisense template
• Move to Travis CI
• Fix issue with test script using wrong pipeline.db when running outside pipeline base dir

Full Changelog: v0.2.1...v0.3.0

Version 0.2.1

• Decreasing disk stress and processing time of the contig step by replacing temporary bam files by pipes (thanks to @karl616)
• Add options for docker so that created files are no longer owned by root (thanks to @leshaker)

Full Changelog: v0.2.0...v0.2.1

Version 0.2.0

• Added ability to resolve relative paths in the index file against its current location
• Change default profile to starrsem
• Set bamSort to samtools in default profile
• Fixed Empty lines in the index file result in a ArrayIndexOutOfBoundsException #7
• Update documentation - resolve #6
• Add genomeIndex parameter - fix #9
• Add samtools index to mergeBam command template
• Add mapping templates for STAR 2.5
• Fix input BAMs considered as paired-end - resolve #14
• Fix error when using both Genome and Transcriptome bams as inputs - fix #13
• Enable trace by default in nextflow config

Full Changelog: v0.1.0...v0.2.0

Version 0.1.0

First version

Full Changelog: https://github.com/guigolab/grape-nf/commits/v0.1.0